Many operators are having a difficult enough time running commuter coaches, let alone all day services. They are often cheaper than the trains for a peak return, but the cost of providing a coach service doesn't really go down in the off peak, where it is then more expensive than the train fare. That also introduces, re-introduces or drastically expands the amount of cash handling done on board coaches, which then means drivers can be responsible for it all day in London. You certainly wouldn't want to take a family on a coach with no child fares available!
The single biggest cause though is traffic, and the resulting unreliability. Many of us regular passengers already take the timetable with a heavy dose of salt - not because the companies are not trying, but because the situation changes from one day to the next. Long term roadworks appear with little or no warning. Monument junction was heavily restricted and all but closed for 6 months for "emergency" gas main works. Then Fenchurch Street was closed for 6 weeks for more "Emergency works" having been open little more than a month. On Friday (26th), Cannon Street was listed for reopening on Sunday 28th after a month's closure. Come yesterday morning, still closed, and the date has suddenly extended for a further month. How can you not know on the day it was due to reopen that you were that far behind? That's before we get to Thames Tunnel, Cycle Superhighways, Uber, planned and unplanned demonstrations in Westminster, accidents, the vagaries of the Blackwall Tunnel, etc. Upon completion of the recent Aldgate gyratory works, all commuter coaches had their permission to stop there and at Aldgate East revoked (on penalty of fines for doing so), because going from two bus stops to one meant there were too many vehicle movements in the morning peak. One of the most useful interchange points removed at a stroke!
Drivers are not easy to come by, and many who are trained simply cannot take the long days (if there are delays, this can take them to the very end of their permitted working hours for the day, usually with no advance warning and requiring staff to be shuffled to ensure services can be covered the following day).
All Commuter services run on LSPs - most, if not all, that run through Canary Wharf have local fares between there and the city. TfL have a different regulatory program to the Traffic Commissioners, requiring 90 days notice rather than 56/70. Despite showing up on TfL's journey planner, there is no real notes (at least not where anyone reads them) that the services do not take any payment form other than cash, and they are often not treated like "red" buses (e.g. permission to use the right turn from Lower Thames Street into Eastcheap).
In sum, the situation just isn't there any more unless you have a large pit of money and lots of patient passengers. I'm surprised those services from the north of London (757, 758, etc.) still run during the day as often as they do.
